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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Transposons01:24

Transposons

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Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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A beginner's guide to manual curation of transposable elements.

Clement Goubert1,2, Rory J Craig3, Agustin F Bilat4

  • 1Canadian Center for Computational Genomics, McGill University, Montreal, Québec, Canada.

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|March 31, 2022
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Summary

This study introduces accessible protocols and tools for manually curating transposable elements (TEs). These resources empower researchers, especially beginners, to generate high-quality TE consensus sequences for genomic analysis.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Generating high-confidence consensus sequences for transposable elements (TEs) is crucial for genomic research.
  • Automated tools exist for identifying potential TE families, but manual curation remains essential for high-quality results.
  • Specialized knowledge for manual TE curation is often informally transferred, limiting accessibility.

Purpose of the Study:

  • To bridge the accessibility gap in manual transposable element (TE) curation.
  • To provide a comprehensive guide for researchers new to the field of TEs.

Main Methods:

  • Development of detailed computer protocols for manual TE curation.
  • Compilation of software recommendations for TE analysis.
  • Creation of video tutorials to guide users through the curation process.
  • Supplementary Methods include step-by-step protocols for beginners.

Main Results:

  • A set of detailed protocols, software recommendations, and video tutorials for manual TE curation has been generated.
  • The provided resources aim to demystify the manual curation process.

Conclusions:

  • The developed resources make manual TE curation accessible to all researchers, particularly those new to the field.
  • This initiative facilitates the generation of high-quality TE consensus sequences, advancing genomic studies.